Protein mutation -- Allow optional small molecules in system generation Modeller

Currently, the system_generation.get_omm_modeller requires a dictionary with the small molecule components. In order for this same function to be used for the protein mutation protocols (and other protocols), we probably want to make the small_mols argument an optional one.

Now, that would make all the component arguments to be Optional, which I think it's fine. That is, this function would allow users to generate an empty OpenMM modeller object if they don't pass any component as an argument.

A workaround this is using an empty dictionary for the small_mols argument.

Locate the system_generation.get_omm_modeller entry point and inspect how its small_mols and other component arguments are handled. Make the component arguments optional so callers can create an empty OpenMM modeller without passing an empty dictionary, then verify existing callers still work and confirm the empty case behaves as intended.